Flood risks are the most frequent natural risks in the world. Their consequences are particularly serious when they affect technical systems in urban areas. Experience feedbacks on guided transport systems show that they are urban technical systems that are particularly vulnerable to this type of natural risk. The resilience concept is used in a systemic approach for making an accurate analysis of this type of natural risk. The purpose of this article is to provide an analysis of guided transport systems’ resilience in the face of flood risks via a study of the failure mechanisms to which component elements of these systems are subjected. By using methods resulting from operational safety concepts and designing a computer tool, all the failure scenarios for components can be produced, together with their domino effects. In this way, our work provides a methodology for characterizing guided transport systems’ vulnerability in the face of natural risks and for comparing this vulnerability depending on whether the system is in an underground, ground-level or overground configuration.